MERmaid only has three main dependencies:
- Boost C++: Base, MPI and filesystem
- An MPI framework: We only test it with openmpi
- Google sparsehash
Currently, we are only running it on 64-bit Linux. Mac OS X is known to have problems building.
make in the top-level directory.
./mermaid output-file-prefix input-files ..
input-files must be a list of FASTQ files using the Illumina 1.3 quality
The outputs will be
- A set of files containing lists of initial k-mers after the initial counting phase. These will be named output-file-prefix.ufx.
- A file containing all the contigs. This will be named output-file-prefix.contigs.0
Mermaid will override default configurations if they are specified in "mermaid.conf". Copy mermaid.conf.example to mermaid.conf and adjust parameter values to override defaults.
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